I noticed that some .asset files are not listed in document, so I ignored them, but now everytime I check out a copy, the Build Settings doesn't get saved, and I need to re-set them (I'm using Unity iPhone btw).

I'm having the same issue. I tried committing all the .asset files in the top-level of the Library directory, but none of them had an impact on the Build Settings. Has anyone found a solution to this problem?

With Unity 3.5 unity as introduced .meta files in Unity3d (was Unity Pro before). You must enable it in

Edit > Project Settings > Editor and switch "Version Control Mode" from "Disabled" to "Meta Files".
This will create a .meta file for each folder and asset and make the project Version Control compatible.

Now, delete "Library" and "Temp" folders if they exist. They must not be versioned and put the on Ignore, so you don't accidentally check them in. The Library folder will be rebuilt once you start Unity3D .